The combination of a proton pump inhibitor (PPI) with two of the following three antibiotics, amoxicillin, clarithromycin, and metronidazole, has been reported to achieve a high eradication rate. These regimens are accepted as standard regimens worldwide. The rationale of PPI-based triple therapy has been established by many clinical trials and a large body of experimental evidence. PPIs have a pivotal effect in the eradication of Helicobacter pylori infection, both indirect effects and direct effects. PPIs have a weak antibacterial effect against H. pylori in vitro, antiurease activity, and anti-ATPase activity. In fact, clinical trials have demonstrated that PPIs alone have a weak eradication effect. Indirect synergistic effects of PPIs could be raising the eradication rate in PPI-based triple regimens. The most potent effects are to stabilize and to raise antibacterial effects of the combined antibiotics, especially clarithromycin and amoxicillin in the hostile gastric environment. These are key antibiotics in an eradication treatment of H. pylori infection. In addition, PPIs have a potent activity to concentrate the antibiotics via suppressing gastric juice. Thus, the indirect effect might be an important role to raise the eradication rate by PPI-based triple therapy in clinical aspects. PPIs have different metabolic pathways, which depend on the CYP enzymes in the liver. Therefore, polymorphism of CYP enzymes might influence eradication rates in PPI-based regimens. The pharmacological characteristics of each PPI including the time exhibiting acid suppressive effect, metabolic pathway, and bioavailability should be considered to achieve a higher eradication rate in PPI-based triple treatment.Helicobacter pylori is recognized as the main etiological factor in the pathogenesis of histologic gastritis, gastric ulceration, duodenal ulceration, gastric MALT lymphoma, and gastric cancer. Treatment to eradicate H. pylori infection has been proven to prevent completely the relapse of gastric or duodenal ulceration and has changed the natural history of ulcer diseases [1][2][3]. Recent strong evidence has demonstrated that the eradication of H. pylori infection might prevent the development of gastric cancer [4]. In addition, the eradication has been proven to improve gastric MALT lymphoma